{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0319JZYS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0319JZYS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0319JZYS](/auxiliary-sets/IGVFDS0319JZYS/) has sequence file(s) [IGVFFI3927LCXN](/sequence-files/IGVFFI3927LCXN/), [IGVFFI8797POIP](/sequence-files/IGVFFI8797POIP/), [IGVFFI4291ESKX](/sequence-files/IGVFFI4291ESKX/), [IGVFFI1384RCQE](/sequence-files/IGVFFI1384RCQE/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0319JZYS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0319JZYS](/auxiliary-sets/IGVFDS0319JZYS/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS0319JZYS/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-13T22:38:44.538418+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3927LCXN/",
"accession": "IGVFFI3927LCXN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:35:55.762873+00:00",
"file_format": "fastq",
"file_size": 22496682,
"href": "/sequence-files/IGVFFI3927LCXN/@@download/IGVFFI3927LCXN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dfc39d1a-e2e6-44b3-863e-d2f3b4958692/IGVFFI3927LCXN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR1-Rep1_S217_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7867OONC/",
"accession": "IGVFFI7867OONC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:27:58.294046+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7867OONC/@@download/IGVFFI7867OONC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/930f1b1a-12c6-4d25-9491-84f6828579cc/IGVFFI7867OONC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8797POIP/",
"accession": "IGVFFI8797POIP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:14.278905+00:00",
"file_format": "fastq",
"file_size": 17334895,
"href": "/sequence-files/IGVFFI8797POIP/@@download/IGVFFI8797POIP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d9548d5b-ab17-4c0b-a5f1-c8b0529d7616/IGVFFI8797POIP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR2-Rep1_S223_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4291ESKX/",
"accession": "IGVFFI4291ESKX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:32.542392+00:00",
"file_format": "fastq",
"file_size": 30283642,
"href": "/sequence-files/IGVFFI4291ESKX/@@download/IGVFFI4291ESKX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b769cc3d-84cf-41f6-9373-6090410687f7/IGVFFI4291ESKX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR3-Rep1_S259_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1384RCQE/",
"accession": "IGVFFI1384RCQE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:36:50.518482+00:00",
"file_format": "fastq",
"file_size": 25189873,
"href": "/sequence-files/IGVFFI1384RCQE/@@download/IGVFFI1384RCQE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/212cfb93-8307-4575-8e5e-083217bd59cf/IGVFFI1384RCQE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR4-Rep1_S265_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1446IYEI/",
"accession": "IGVFFI1446IYEI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:12.941557+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1446IYEI/@@download/IGVFFI1446IYEI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1ff34b94-983c-44a7-b74f-1c3f9bf4f549/IGVFFI1446IYEI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0717WSTW/",
"accession": "IGVFFI0717WSTW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:27.403902+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI0717WSTW/@@download/IGVFFI0717WSTW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5c6165a7-3847-4a1f-8f27-b75bc7601575/IGVFFI0717WSTW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6982FUBD/",
"accession": "IGVFFI6982FUBD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:41.197659+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6982FUBD/@@download/IGVFFI6982FUBD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/bb8c1480-e476-44f4-b97a-283171c69696/IGVFFI6982FUBD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6376TFTJ/",
"accession": "IGVFDS6376TFTJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:07:50.695939+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9315IOJD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9315IOJD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of CCND1) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:35:55.762873+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a9c09edc-8211-4f32-8341-8035c2aa8f46"
}